Leishmaniasis is a neglected tropical disease endemic in over 90 countries. The disease has two main pathologies; cutaneous leishmaniasis (CL) that generally self-heals, and visceral leishmaniasis (VL) that is fatal if untreated. The majority of VL cases, concentrated on the Indian subcontinent (ISC) and East Africa, are caused by . However, recent foci of CL on the ISC have been attributed as an atypical phenotype of . including a recent outbreak in Himachal Pradesh, India. Whole genome sequencing and phylogenetic analysis was undertaken to investigate the origins and genetic factors leading to this pathology atypical of . . Here we demonstrate the isolate from Himachal Pradesh is derived from a genetic hybridization between two independent . parents from the 'Yeti' ISC1 divergent clade of parasites, identified in the Nepalese highlands. This reveals that intraspecies . hybrids can give rise to a novel strain associated with CL.